Genetic Diversity Values Research Articles

Genetic Distance for Genotype Barley ( Hordeum vulgare L.) using RAPD-PCR Technology.

Abstract. The study targets to know the genetic Distance of fifteen genotypes of six-row barley (Ibaa99 , Alhadar , Alkheer , Alwarkaa , Buraq , Amal , Shuaa , Rehan , Samir , Arevate , Acsad1811 , Acsad1816 , Acsad1818 , Acsad1827 , Acsad1840 ) Based on the RAPD technique using fifteen primers, The primers used produced 111 band, including 94 band for variant alleles, with a rate of 84.68%, The molecular weights of the prefixes ranged between 200-2000 bp,. The primer OPB-14 gave the highest number of variant sites, reaching 10 bands, and a high discriminatory ability of the primer, which amounted to 10.64, the highest percentage of variant alleles in the primers (OP B-14, OP C-08, OP D-03, OP D-18, and OP F-05) was (100%), and the primer OP C-16 gave the highest efficiency of 11.209. The genetic divergence values showed that the largest genetic divergence was between the Alkheer cultivar and the Acsad1840 genotype (49.00), while the least genetic divergence was between the two genotypes Acsad1818 and Acsad1827, with a value of (9.00), In addition, the results of the kinship tree analysis of the genotypes were divided into two main groups, where Ibaa99 were in the first main group, while the other genotypes were in the second main group. From the results obtained, it is possible to rely on genetically divergent structures in breeding programs by introducing them into crosses with other varieties to obtain good productive characteristics.

Inference on the biological history of the Comoros archipelago using the CD4 Alu/STR compound system

The Comoros Archipelago is located at the northern end of the Mozambique Channel between Madagascar and the East African coast. Its settlement would have been influenced by contacts and possibly migratory waves that would have come from the East African coast, Middle East and Southeast Asia. This finding was the conclusion of various previous genetic studies carried out on Comorian populations to answer the question of its settlement and its biological history. These studies have used many kinds of molecular markers, although the autosomal markers (Alu/STR CD4) used in the present study have never been studied on the archipelago's populations. Nevertheless, they have been used on populations all over the world and have provided valuable information on genetic affinities and differentiation between populations and have also shed more light on the origins of modern human.In this study, we aimed to characterize for the first time the populations of the 3 main islands of the Comoros Archipelago using the CD4 Alu/STR compound system. Due to its robustness, this system allowed us to include, in our comparative analyses, populations having shared a common history with Comoros islanders (through migrations, commercial relations, or others).Our results showed by island, peculiar frequencies of STR and Alu alleles, as well as haplotypic ones. Genetic diversity values at the allelic level, ranged between 0.798 and 0.836 for the STR, and between 0.254 and 0.327 for the Alu. The most frequent haplotypes were 85+, followed by 115+ and 120+ in all the three islands. Phylogenetic and comparative analyses highlighted that our populations exhibit more affinities with sub-Saharan populations especially the Kenyans. However some Middle Eastern signals are perceptible in Anjouan Islanders through 90+ and 110− haplotypes.Finally, the results obtained contribute to a further understanding of the biological history of the Comoros population and provide new insights into the gene flows such as haplotypes of Middle Eastern origin.

Estimating the Genetic Diversity of Oranges Citrus spp. in South Sulawesi, Indonesia, Using RAPD Markers

Oranges hold significant economic importance, being cultivated extensively worldwide and having a large global market. Indonesia, ranked eighth globally as a producer of oranges, is one of the countries with high genetic diversity of oranges. This diversity is distributed across various regions of Indonesia, including South Sulawesi. Despite the advancements in DNA-based molecular marker techniques for assessing genetic diversity, information on orange diversity in South Sulawesi is currently unavailable and under-researched. In this study, random amplified polymorphic DNA (RAPD) markers were utilized to analyze the genetic diversity of oranges in five production centers in South Sulawesi. Leaf samples of 13 orange varieties were collected from the five production centers: Pangkep, Sidrap, Bantaeng, North Luwu, and Selayar in South Sulawesi, Indonesia. Genomic DNA extraction from the orange leaves followed the protocol of the DNA Mini Kit Geneaid. DNA amplification was carried out using the RAPD method with 14 primers: OPE-04, OPH-04, OPH-15, OPN-14, OPN-16, OPR-08, OPR-20, OPW-06, OPW-09, OPX-07, OPX-11, OPX-17, UBC-18, and UBC-51. The RAPD primers yielded 109 amplified fragments ranging in size from 200 to 2000 base pairs (bp), and all RAPD primers showed 100% polymorphism. The genetic diversity value (He) of oranges in South Sulawesi was moderate (0.236). Cluster analysis based on a similarity coefficient of 77% divided the 175 orange genotypes into five groups. The most closely related genotypes were SB6 and SB7, exhibiting 100% similarity, followed by genotypes JS8 and JS9 and JS13 and JS17, with genetic similarities exceeding 99% for each pair. Genotypes P9 and SI5 displayed the highest genetic distance, with a similarity coefficient of 57%. The dendrogram diagram can serve as a basis for selecting desired plant traits in the improvement of plant characteristics through both conventional breeding and genetic engineering activities.

Genetic polymorphism of populations and phylogeny of the Central Siberian Polygonum (Polygonaceae) section using ISSR and chloroplast markers

This article is devoted to the study of genetic polymorphism of populations and phylogeny of Polygonum section using ISSR and chloroplast markers. Section Polygonum is a taxonomically complex group. Identification of individuals is complicated because of the small size of plants, the processes of interspecific hybridization, heterocarpy, phenological and ecological plasticity. In this work, the genetic variability of six populations of five knotweed species growing in Krasnoyarsk was studied. ISSR analysis revealed that the level of genetic diversity in the populations varies from 4.17 % to 35.83 % and has maximum values for genetically close species P. sabulosum (P = 35.83 %) and P. arenastrum (P = 22.5–30 %). Minimum values of genetic diversity were observed for populations of P. aviculare (P = 4.17 %) and P. calcatum (P = 5 %). The studied populations are characterized by a very high level of genetic differentiation (Gst = 0.78) and reliably belong to different species. On the similarity dendrogram (UPGMA), individuals of these species form clearly distinct clades. The genetic structure of populations using STRUCTURE also shows a reliable division of individuals into 5 clusters corresponding to the studied species. Phylogenetic analysis using the trnL-trnF chloroplast region shows the presence of a 5-nucleotide deletion and two transversions that makes it possible to divide the studied group of Polygonum into two morphologically different clusters. The first group is formed by P. arenastrum, P. calcatum, P. caspicum, P. sabulosum and characterized by the absence of a main shoot, a gradual reduction of leaves to the top of shoots and the perianth dissection by 1/2 of its length. The second group includes P. aviculare, P. boreale, P. neglectum, P rectum that have a main shoot, heterophilly, perianth dissection by 2/3–3/4 of its length. Two substitutions have been identified in the matK sequences, however it is less informative for solving taxonomic issues of the studied group.

Genetic diversity in leucine-rich repeats (LRR) of toll-like receptor-2 and -4 genes in three species of South American camelids

Toll-like receptors (TLRs) are responsible for the innate immune response to detect and activate pathways against pathogens in animals. Polymorphisms within these genes have been related to susceptibility or resistance to different diseases. A high variability present in these sequences allows the population to develop a better adaptive potential while the opposite will make them more susceptible to new diseases. This variability decrease may occur because of external factors such as bottlenecks or artificial selection. The objective of this study was to verify the genetic diversity in the leucine-rich repeats (LRR) of TLR2 and TLR4 in three species of camelids from the new world. The genetic diversity was evaluated in the LRR of the TLR2 and TLR4 genes of 120 individuals that belong to the population of alpacas (Vicugna pacos), llamas (Lama glama) and vicuñas (Vicugna vicugna). Different polymorphisms were found, as well as the possible parental sequences and haplotype frequencies. Genetic diversity values, the degree of population differentiation, and amino acid variations were analyzed. The tests showed a very low genetic diversity (TLR2, π = 0.00525; TLR4, π = 0.00118) but a medium-high haplotype diversity (TLR2, Hd=0.923; TLR4, Hd=0.476) among the three species analyzed. There are both polymorphisms and haplotypes that are shared between these species and private haplotypes for each species. The demographic fixation index indicates no gene flow between groups of animal populations. Certain amino acid changes detected in the protein structure change its characteristic of it, making this to be a harmful variation. These results suggest that years of interference in the natural development of South American camelids have led to a drastic decrease in the diversity of their TLRs.

Genetic Diversity of Bananas (Musa spp.) in Pesawaran District, Lampung Province Based on Sequence Related Amplified Polymorphism (SRAP) Marker

Banana (Musa spp.) is a leading commodity that makes a major contribution to national fruit production. One of the districts in Lampung Province which has a significant contribution to Indonesia's banana production is Pesawaran Regency. The molecular marker used in this study is Sequence-Related Amplified Polymorphism (SRAP). This study aims to determine the genetic diversity of bananas, determine the suitable combination of SRAP primers to determine the genetic diversity of bananas and determine the similarity relationship of bananas in the Pesawaran District. The total genomic DNA was extracted using DNeasy Plant Mini Kit (Geneaid) according to the protocol from the manufacturer followed by their amplification using SRAP primers. Similarity analysis was carried out based on similarity index values and dendrogram construction using the NTSYS 2.0 program. Research results show that a total of 204 loci (167 polymorphic loci and 37 monomorphic loci) were obtained from 9 selected primer combinations. The genetic diversity of 19 banana cultivars originating from Pesawaran Regency resulted in low genetic diversity values (0-0.27). Banana kinship based on Sequence Related Amplified Polymorphism (SRAP) markers divided 19 banana cultivar samples and 4 wild banana samples into 2 large clusters with similarity coefficient values between 0.70-0.97.

Exploring agro-morphological profiles of Phaseolus vulgaris germplasm shows manifest diversity and opportunities for genetic improvement

Common bean (Phaseolus vulgaris) is a seed crop with huge potential to contributing to food security in developing countries. In crop improvement, assessing genetic variability is a decisive step, requiring characterization of available crop germplasm. The present study aims at characterizing 39 common bean genotypes from various locations in Cameroon and five from Kenya using 19 qualitative and 36 quantitative traits of high descriptive values. Diversity among germplasm was assessed by determining diversity indices and carrying out multivariate analysis. Seventeen out of the nineteen qualitative traits (89.47%) were polymorphic, displaying each at least two phenotypic classes. High diversity was found. Average observed and expected number of phenotypic classes per trait were 3.74 and 2.53 respectively. Nei's genetic diversity value of 0.49 and Shannon-Weaver diversity index estimates of 0.74 were found. Significant differences were observed among genotypes for all measured quantitative traits. Yield traits showed significant correlation with other related quantitative traits. Cluster analysis separated the studied germplasm into three distinct groups, with the clustering pattern not showing any connection with location. The test of equality revealed significant difference between these clusters for most quantitative traits. Mahalanobis D2 statistics revealed germplasm of cluster I and III as potential parents for future breeding programs. This study identified genotypes with desirable agronomic traits such as higher number of seeds per pod, lower number of days to maturity, higher number of pods per plant, and higher yield. These and other important discriminatory traits are discussed and proposed for genetic improvement of common bean.

Genetic Diversity and Population Structure in Ethiopian Mustard (Brassica carinata A. Braun) as Revealed by Single Nucleotide Polymorphism Markers.

Ethiopian mustard (Brassica carinata A. Braun) is currently one of the potential oilseeds dedicated to the production for biofuel and other bio-industrial applications. The crop is assumed to be native to Ethiopia where a number of diversified B. carinata germplasms are found and conserved ex situ. However, there is very limited information on the genetic diversity and population structure of the species. This study aimed to investigate the genetic diversity and population structure of B. carinata genotypes of different origins using high-throughput single nucleotide polymorphism (SNP) markers. We used Brassica 90K Illumina InfiniumTM SNP array for genotyping 90 B. carinata genotypes, and a total of 11,499 informative SNP markers were used for investigating the population structure and genetic diversity. The structure analysis, principal coordinate analysis (PcoA) and neighbor-joining tree analysis clustered the 90 B. carinata genotypes into two distinct subpopulations (Pop1 and Pop2). The majority of accessions (65%) were clustered in Pop1, mainly obtained from Oromia and South West Ethiopian People (SWEP) regions. Pop2 constituted dominantly of breeding lines and varieties, implying target selection contributed to the formation of distinct populations. Analysis of molecular variance (AMOVA) revealed a higher genetic variation (93%) within populations than between populations (7%), with low genetic differentiation (PhiPT = 0.07) and poor correlation between genetic and geographical distance (R = 0.02). This implies the presence of gene flow (Nm > 1) and weak geographical structure of accessions. Genetic diversity indices showed the presence of moderate genetic diversity in B. carinata populations with an average genetic diversity value (HE = 0.31) and polymorphism information content (PIC = 0.26). The findings of this study provide important and relevant information for future breeding and conservation efforts of B. carinata.

The Qatari population's genetic structure and gene flow as revealed by the Y chromosome.

The Y-chromosome has been widely used in forensic genetic applications and human population genetic studies due to its uniparental origins. A large database on the Qatari population was created for comparison with other databases from the Arabian Peninsula, the Middle East, and Africa. We provide a study of 23 Y-STR loci included in PowerPlex Y23 (Promega, USA) that were genotyped to produce haplotypes in 379 unrelated males from Qatar, a country at the crossroads of migration patterns. Overall, the most polymorphic locus provided by the Promega kit was DYS458, with a genetic diversity value of 0.85 and a haplotype diversity of 0.998924. Athey's Haplogroup Predictor tool was used to predict haplogroups from Y-STR haplotypes in the Qatari population. In a median-joining network, the haplogroup J1 predominance (49%) in Qatar generated a star-like expansion cluster. The graph of population Q-matrix was developed using Y-STR data from 38 Middle Eastern and 97 African populations (11,305 individuals), and it demonstrated a stronger sub-grouping of countries within each ethnic group and showed the effect of Arabs on the indigenous Berbers of North Africa. The estimated migration rate between the Qatari and other Arabian populations was inferred using Bayesian coalescence theory in the Migrate-n program. According to the Gene Flow study, the main migration route was from Yemen to Kuwait through Qatar. Our research, using the PowerPlex Y23 database, shows the importance of gene diversity, as well as regional and social structuring, in determining the utility of demographic and forensic databases.

Characterization of prolamin storage protein profiles in Tunisian pearl millet landraces toward better utilization and improvement

AbstractBackground and ObjectivesThis study reports for the first time the variation of prolamin profiles among 51 pearl millet landraces representing seven populations prospected from contrasted bioclimatic areas of Tunisia.FindingsA total of 27 prolamins bands were detected, ranging from 11 to 245 kDa. Among them, 14 were polymorphic, resulting in a polymorphism rate of 51.85%. The bands with lower molecular weights are the most frequent. The biochemical marker M25.4 showed the highest value of Nei genetic diversity (h = 0.500), Shannon information index (I = 0.693), and effective number of alleles per locus Ne (2). At the population level, the polymorphism rates ranged between 50% (Mahdia) and 92.86% (Hammem Jebli, Kairouan, Medenine). The population of Kairouan showed the highest genetic diversity indices (I = 0.511 ± 0.054, h = 0.345 ± 0.041), while the lowest levels were recorded for the population of Mahdia (I = 0.268 ± 0.076, h = 0.177 ± 0.052). Analysis of molecular variance analysis indicated that the highest amount of genetic diversity was encompassed within the studied populations (89%). This was supported by low genetic differentiation (PhiPT = 0.110, p = .029) and Nei genetic distance values. The classification pattern using ward dendrogram and factorial analyses revealed the distinction of two clusters with a low genetic structure based on the geographic origins of landraces.Significance and NoveltyThe detected biochemical protein polymorphism could be a highly effective tool for the genetic resources characterization of pearl millet landraces, which will be further utilized in breeding investigations and taxonomic surveys of this cereal crop.

Wolf genetic diversity compared across Europe using the yardstick method

Integrating data across studies with traditional microsatellite genetic markers requires careful calibration and represents an obstacle for investigation of wide-ranging species where populations require transboundary management. We used the “yardstick” method to compare results published across Europe since 2002 and new wolf (Canis lupus) genetic profiles from the Carpathian Mountains in Central Europe and the Dinaric Mountains in Southeastern Europe, with the latter as our reference population. We compared each population with Dinaric wolves, considering only shared markers (range 4–17). For each population, we calculated standard genetic diversity indices plus calibrated heterozygosity (Hec) and allelic richness (Ac). Hec and Ac in Dinaric (0.704 and 9.394) and Carpathian wolves (0.695 and 7.023) were comparable to those observed in other large and mid-sized European populations, but smaller than those of northeastern Europe. Major discrepancies in marker choices among some studies made comparisons more difficult. However, the yardstick method, including the new measures of Hec and Ac, provided a direct comparison of genetic diversity values among wolf populations and an intuitive interpretation of the results. The yardstick method thus permitted the integration of diverse sources of publicly available microsatellite data for spatiotemporal genetic monitoring of evolutionary potential.

Genetic diversity and climatic suitability over time of Baetodes huaico (Ephemeroptera: Baetidae)

In the Neotropical region, the genetic diversity and bioclimatic preferences of Ephemeroptera are poorly known mainly due to the lack of studies. We used the 16S rRNA mitochondrial gene to examine the genetic structure of Baetodes huaico, an aquatic insect distributed in the Northwest of Argentina. Also, we performed an ecological niche modeling (ENM) to understand bioclimatic preferences and combine with the genetic data to understand historical dynamic distribution of B. huaico. We found that B. huaico populations are genetically structured into two distinct geographic groups. The ENM showed a distributional shift from south to north through time. Also, we recovered a stable region over time in the Southwest of Tucumán with the highest value of suitability and high genetic diversity; this region was previously proposed as a Pleistocene refuge. Our result suggests that the northern group was stable over time and underwent a recent demographic expansion coincident with a glacial refugium, whereas the southern group could have been affected by climatic fluctuations during. The results emphasize possible climatic influences in genetic population differentiation, and contributes to the knowledge of the genetic diversity of Ephemeroptera from subtropical Argentina laying the groundwork for future work for other freshwater insects in our region.

Agro-morphological and nutritional assessment of chenopod and quinoa germplasm-Highly adaptable potential crops.

Quinoa belongs to the family Chenopodiaceae, a pseudo-grain having high nutritional value and is considered an underexploited vegetable crop with the potential to improve the nutritional security of millions. Therefore, assessing genetic diversity in Chenopodium germplasm to untap nutritional and site-specific adaptation potential would be of prime importance for breeders/researchers. The present study used 10 accessions of two Chenopodium species, that is, C. quinoa and C. album. Quantitative and qualitative phenotypic traits, proximate composition, minerals, and amino acids profiles were studied to compare the differences in nutritional value and extent of genetic diversity between these two species. Our results showed significant variation existed in yield attributing agro-morphological traits. All the traits were considered for hierarchical clustering and principal components analysis. Large genetic variability was observed in traits of Chenopodium accessions. The protein, dietary fiber, oil, and sugar content ranged from 16.6% to 19.7%, 16.8% to 26%, 3.54% to 8.46%, and 3.74% to 5.64%, respectively. The results showed that C. album and C. quinoa seeds had good nutritional value and health-promoting benefits. The C. quinoa was slightly ahead of than C. album in terms of nutritional value, but C. album accession IC415477 was at par for higher test weight, seed yield (117.02 g/plant), and other nutritional parameters with C. quinoa accessions. IC415477 and other potential accessions observed in this study may be taken up by breeders/researchers in the near future to dissect nutritional value of Chenopodium and related species for dietary diversity, which is imperative for the nutritional security of the ever-growing world's population.

Building a Teleost Fish Traceability Program Based on Genetic Data from Pacific Panama Fish Markets.

Fish tissue samples from 203 adult individuals were collected in the main ports and markets of the Pacific coast of Panama. Molecular identification based on a cytochrome oxidase I gene segment of all species was verified by GENBANK reference sequences. A total of 34 species from 14 families (Ariidae, Caranjidae, Centropomidae, Gerreidae, Haemulidae, Lobotidae, Lutjanidae, Malacanthidae, Mugilidae, Scianidae, Scombridae, Serranidae, Sphyraenidae, Stromateidae) were identified at the species level from 164 sequences. Additionally, three Caribbean species were molecularly identified among the analyzed samples (Mycteroperca xenarcha, Paralonchurus brasilensis and Lobotes surinamensis). Species diversity was slightly higher in the Gulf of Panama than in the Gulf of Chiriquí. For species with five or more individual sequences, genetic diversity and genetic connectivity parameters such as total number of haplotypes (H), haplotype diversity (Hd), and nucleotide diversity (π) were calculated. Overall, pelagic-migratory species showed higher values of genetic diversity than coastal and estuarine species with some exceptions. Connectivity between Gulf areas was compared using values of genetic distances and genetic differentiation (Fst). The high level of connectivity observed between the Gulf of Chiriqui and the Gulf of Montijo indicates the existence of a single stock in that area for the following species: Scomberomorus sierra, Caranx caninus and Lutjanus guttatus. The demographic history of the most common species was examined using Tajima's D values, suggesting population expansion for two snapper species, L. peru and L. argentiventris, having significant and higher values. Another important contribution from this research was the production of primers and dual-labeled probes for environmental DNA detection using qPCR for the five most abundant species (spotted rose snapper, yellow snapper, green jack, Pacific crevalle jack and the Pacific sierra fish). These markers represent a new set of tools for environmental DNA (eDNA) detection and molecular traceability of three commercially important fish species along the supply chain including landing sites and markets of the main fishery areas.

Natural Hybridization between Bursera bicolor × B. glabrifolia (Burseraceae) Complex: Molecular and Chemical Evidence

The hybridization phenomenon is recognized as an important evolutionary force that influences the diversification and evolution of different vascular plant groups. Hence, it is important to identify hybrid individuals. In Mexico, the dry tropical forest (DTF) is considered as the main center of diversification and endemism of the Bursera genus, containing 85% of the approximately 106 described species worldwide. In the Mexican DTF, a complex of Bursera species was identified, which is formed by two putative parental species Bursera bicolor (Will. ex Schltdl.) Engl. and B. glabrifolia (H.B.K) Engl. Their putative hybrids were analyzed using molecular (cpSSR) and chemical markers (monoterpenes, sesquiterpenes, and triterpenes) in two pure sites (one site for each parental species) and two hybrid zones. We tested whether individuals with atypical morphology between B. bicolor and B. glabrifolia from sympatric sites were the result of genetic flow between these two species. A total of 80 individuals were analyzed with 4 microsatellite diagnostic primers and 37 secondary metabolites (SMs). The genetic and chemical markers were highly coincident according to the statistical analyses performed, and they supported the hybridization hypothesis in this Bursera complex, with both species remaining distinct even in sympatric zones. α-Amyrin (b), β-amyrin (a), and β-amyrin (b) (triterpenes) were the SMs that most contributed to differentiating putative parental species according to SIMPER analysis. The putative hybrids registered the highest genetic diversity values along with the highest number of SMs, out of which 11 were novel and distributed as follows: triterpenes > monoterpenes > sesquiterpenes. Finally, the chemical markers of the three analyzed families give a framework for future studies to explore hybridization events between Bursera species.

Mountains as refugia in the Dry Chaco: phylogeography and species distribution modelling of the southernmost chilli pepper, Capsicum chacoense Hunz. (Solanaceae)

Abstract Phylogeographical studies combined with species distribution modelling can provide evidence for past climate refugia. During the Pleistocene, the Chaco phytogeographical province (ChPP) underwent changes in the distribution range, and the flora might have found refugia in different habitats according to their climatic requirements. This contribution aims to infer the effects of historical geoclimatic changes on the evolutionary history of Capsicum chacoense, the southernmost chilli pepper growing in the ChPP. We analysed 27 localities with plastid markers and 23 with nuclear markers, covering the geographical range of the species. We performed statistical phylogeography, in addition to current and past species distribution modelling. We found three haploclades, diverging 2.3–1 Mya, intermingled throughout the mountain ranges of the ChPP as a consequence of glacial cycles. According to the species distribution modelling, the expansion of the species distribution occurred during interglacial periods. We found two dispersal routes from south to north of the species distribution, concomitant with the migration routes of birds that disperse their fruits. The spatial distribution of genetic diversity showed the highest genetic diversity values at higher elevations. The main orographic systems of the study area were identified as areas of presumed population stability. Consequently, mountains are priority regions for conservation because they contain areas with high genetic diversity.

Genetic diversity of wedgefishes and guitarfishes at landing sites in east Indonesia using Cytochrome Subunit I (COI)

Abstract. Tapilatu ME, Wijayanti DP, Subagiyo, Sembiring A, Yusmalinda NLA, NIngsih EY, Malik MDA, Pertiwi NPD. 2023. Genetic diversity of wedgefishes and guitarfishes at landing sites in east Indonesia using Cytochrome Subunit I (COI). Biodiversitas 24: 3120-3127. Wedgefish and guitarfish are considered endangered and protected by law in Indonesia due to pressure from overexploitation. They are highly exploited because of their economic value. This condition impacts the decline in the number of populations to the value of genetic diversity. This study used mitochondrial DNA to assess the genetic diversity of wedgefishes and guitarfishes which landed in the eastern part of Indonesia. We found Rhynchobatus australiae (Whitley, 1939) to be the most common species (14 out of 26 sequenced samples), with Glaucostegus typus (Bennett, 1830) and Rhinobatos jimbaranensis (Last, White, & Fahmi, 2006) appearing infrequently. COI sequences were obtained from the NCBI database and utilized in the study to compare population differentiation. Among the R. australiae populations, the results showed that the genetic diversity (Hd) values from Papua, Bali, and Lombok were 1.00, 0.67, and 0.75, respectively. In Papua, G.typus populations showed genetic diversity values of 0.90. R. jimbaranensis from Bali showed a genetic diversity of 0.50. Papua populations indicated higher genetic diversity than Bali and Lombok populations. Furthermore, the analyses of pairwise FST values and AMOVA indicated moderate genetic divergence across reference populations of R. australiae and G. typus in this study. Based on this value, a cautious conservation strategy in optimizing fisheries management will be required to limit anthropogenic impacts.

Genetic diversity of the stag beetle, Lucanus cervus (Insecta, Coleoptera) in Romania based on ND1 mitochondrial sequences

Lucanus cervus (Linnaeus, 1758) is one of the largest Coleoptera species in Europe and one of the most recognizable. It is a saproxylic species living in woodlands and wooded urban habitats and spending its larval stages inside tree trunks below or near soil level, feeding on decaying wood. The stag beetle has a wide distribution covering the entire Europe up to the Ural Mountains. In this paper, we attempted to describe the diversity and genetic structure of L. cervus populations in Romania using the NADH mitochondrial molecular marker. We identified 36 haplotypes arranged in a star-shaped structure with a central haplotype shared by many samples and linked by one or two mutational steps with other 35, represented by 1–3 samples. This pattern is frequently attributed to populations that have undergone recent range expansion, a phenomenon which is also sustained by the mismatch analysis. The analyzed populations revealed various degrees of genetic diversity. Many populations with relatively high levels of genetic diversity were found outside the Natura 2000 Network Special Areas of Conservation, while some populations included in protected areas proved to have low values of genetic variability. This underlines the need to review the designated protection sites for this species in Romania.

Genomic Patterns of Iberian Wild Bees Reveal Levels of Diversity, Differentiation and Population Structure, Supporting the “Refugia within Refugia” Hypothesis

We used a population genomic approach to unravel the population structure, genetic differentiation, and genetic diversity of three widespread wild bee species across the Iberian Peninsula, Andrena agilissima, Andrena flavipes and Lasioglossum malachurum. Our results demonstrated that genetic lineages in the Ebro River valley or near the Pyrenees mountains are different from the rest of Iberia. This relatively congruent pattern across species once more supports the hypothesis of “refugia within refugia” in the Iberian Peninsula. The results for A. flavipes and A. agilissima showed an unexpected pattern of genetic differentiation, with the generalist polylectic A. flavipes having lower levels of genetic diversity (Ho = 0.0807, He = 0.2883) and higher differentiation (FST = 0.5611), while the specialist oligolectic A. agilissima had higher genetic diversity (Ho = 0.2104, He = 0.3282) and lower differentiation values (FST = 0.0957). For L. malachurum, the smallest and the only social species showed the lowest inbreeding coefficient (FIS = 0.1009) and the lowest differentiation level (FST = 0.0663). Overall, our results, suggest that this pattern of population structure and genetic diversity could be explained by the combined role of past climate changes and the life-history traits of the species (i.e., size, sociality and host-plant specialization), supporting the role of the Iberian refugia as a biodiversity hotspot.

Genetic diversity, heritability, and productivity of new sugarcane (Saccharum officinarum L.) clones on paddy fields for enhanced sugar production in Indonesia

Sugar production in Indonesia has decreased by 2.12 million tons (4.65%) in 2020 due to the limited supply of superior varieties. The purpose of this study was to understand the potential of the expected superior clones before being released as new superior varieties. This study was conducted in Sidoarjo, Indonesia which has alluvial soil types. This study used a randomized block design (RBD) with one treatment factor (clone) consisting of clones SB01, SB03, SB04, SB11, SB12, SB19, SB20, and varieties PS 881, and MOJO. Data analysis used 5% ANOVA, 5% least significance difference test, correlation test, genetic diversity test, and heritability test. The results of the analysis showed significant differences with all treatments at 48, 50, and 52 weeks after planting (WAP) in the variable brix while the sugarcane stems weight, rock crystal, and yield were significantly different only at 52 WAP which were tested in multilocation in paddy fields and alluvial soil types. Clone SB01 showed the highest brix value of 26.88%, the highest stem weight of 149.20 tons/ha, the highest yield of 10.63%, rock crystal 15.87 tons/ha, the value of genetic diversity in the moderate category was seen in crystal characters (12.55 %), phenotypic diversity in the moderate category was seen in crystal characters (14.364%) and the heritability value was in the fairly high category in brix characters (0.96%). This study shows that the characters inherited from their parents are relatively stable.